tbuckley/cabot-search huggingface dataset:
EPCO-20. EXPLORATION OF DNA METHYLATION PATTERNS IN GLIOBLASTOMA REPROGRAMMED MICROGLIAL CELLS
Authors: Lorraine Richart, Camille Cialini, Tony Heurtaux, Tanja Müller, Ann-Christin Hau, Michel Mittelbronn
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is the most frequent and malignant adult-type diffuse glioma (WHO grade IV) with a median patient survival of less than 15 months despite multimodal treatment. The poor prognosis of GBM, among others, is associated with a tumor-supporting microenvironment characterized by a rather anti-inflammatory state, where the tumor cells have been shown to hijack microglial gene expression profiles. These so-called tumor-associated microglia cells (TAMs) repress normal immune functions, such as phagocytosis and pro-inflammatory cytokine secretion through transcriptional reprogramming, further underlying morphological changes. It is currently starting to emerge that the exceptional cellular plasticity required to orchestrate such microglial reactivity could originate from pre-imposed epigenetic modifications. We thus hypothesize that TAM reprogramming in GBM is controlled by epigenetic mechanisms, and therefore aim to understand if modifications in DNA methylation patterns can lead to pro-tumor transcriptomic and phenotypical changes.Reactive microglia are classically described as either ‘pro-inflammatory’ M1 or ‘anti-inflammatory’ M2 phenotypes, inducable by Lipopolysaccharide (LPS) and Interferon-gamma (IFNɣ) or Interleukin-4 (IL-4), respectively. In a GBM context, microglial cells have been mostly classified as M2, but exhibit heterogeneous features among the M1 to M2 activation spectrum. In this study, we exposed human and murine microglial cell lines to LPS, IFNɣ, IL-4, and GBM-conditioned medium (GBM-CM), followed by morphological assessment, transcript expression and secretome characterization. The onset of activation was followed in time series every 12h to interrogate epigenetic and transcriptomic changes together with protein expression and secretion. After exposure to GBM-CM, microglial cells exhibited a bipolar and more elongated phenotype. We observed significant variations in cytokine production together with a decrease in phagocytosis in LPS-treated microglia, whereas the secretome in GBM-CM was only slightly altered. We furthermore observed differentially methylated regions (DMRs) using the novel Infinium® Mouse Methylation BeadChip, suggesting a role of DNA methylation in microglial reprogramming.
BIOM-45. DETERMINANTS OF GBM VULNERABILITY TO INHIBITORS OF NEDD8 ACTIVATING ENZYME (NAE)
Authors: Nanyun Tang, Yue Hao, Michael Berens
Journal: Neuro-Oncology (2022)

Abstract Advancing new therapeutics to FDA approval for GBM is hampered by intra- and inter-tumoral heterogeneity. Design of clinical trials to enroll patients likely to respond to a new treatment seems critical to build the arsenal of agents against this disease. Neddylation is a protein modification pathway aligned to protein degradation and cytological localization within the ubiquitin/proteasome system. Components of the neddylation pathway are frequently overexpressed or hyperactivated in GBM, and whose upregulation has been associated with glioma progression and worse survival. Among glioblastoma cell lines and patient-derived stem cells, subsets were found to be selectively susceptible to NAE inhibitors. We previously showed that PTEN signaling, DNA replication, and chromatin instability pathways are the most significant differentiators between MLN4924 sensitive vs. non-sensitive models. To test a candidate molecular “signature of vulnerability”, two subsets of PDX models (PTEN wildtype and PTEN del or mutated) were treated with a panel of 3 NAE inhibitors. 5 GBM PTENwt models were shown vulnerable to MLN4924 and TAS4464 with average EC50 values 5-10 folds lower than 6 PTENmt/del models. CDC activity was greater against PTENwt, but only 2-fold different vs PTENmt/del. Transcriptomic data mining uncovered additional determinants of response to NAE inhibitors. To disclose the relationship between constitutive expression of three gene sets: DNA Replication Fork Progressing, Replication Fork Protection, and Replication Fork Protection Complex, we found that the genes involved in these are significantly under expressed in PTENmt models when comparing to PTENwt models. The molecular determinants of drug response to NAE inhibitors will be further verified in the extended preclinical models and lead to a patient-enrollment “signature of vulnerability” to increase the likelihood of demonstrating therapeutic efficacy in the early stage of clinical trials.
EPCO-40. INFRATENTORIAL NF2 MUTANT SPORADIC MENINGIOMAS DIFFER FROM THOSE IN SUPRATENTORIAL LOCATIONS AND ARE MORE BENIGN
Authors: Sagar Vasandani, Shaurey Vetsa, Muhammad Jalal, Kanat Yalcin, Neelan Marianayagam, Arushii Nadar, Lan Jin, Robert Fulbright, E Zeynep Erson-Omay, Murat Günel, Jennifer Moliterno
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Approximately 50% of sporadic meningiomas, which originate throughout the neuroaxis, harbor bi-alleic NF2 loss. We sought to determine whether NF2 mutant meningiomas originating from different intracranial locations relative to the tentorium differ with regards to their genomic profile and clinical behavior. METHODS Clinical and whole exome sequencing data (WES) for all patients who underwent resection of NF2 mutant meningiomas and consented to WES were reviewed and analyzed. RESULTS 258 NF2 mutant meningiomas were included and subdivided into supra- (sNF2) versus infra-tentorial (iNF2) groups (230 versus 28, respectively). Supratentorial location was significantly associated with genomically unstable tumors (percent genome altered median 12% vs. 1%, p&amp;lt; 0.001) and were more likely to harbor the more aggressive feature of chromosome 1p deletion (31.4% vs. 8.3%, p= 0.036). These malignant genomic features correlated with an increased incidence of high risk clinical features, including higher-grade (i.e. WHO Grade II/III) (48.9% vs. 7.14%, p &amp;lt; 0.001) and elevated Ki-67 (58.9% vs. 16.6%, p&amp;lt; 0.01), as well as larger volume (median 26.21 cm3 vs. 9.84 cm3, p&amp;lt; 0.001) and edema (65.8% vs. 25.9%, p= 0.001) in sNF2 meningiomas as compared with iNF2 tumors, respectively. Not surprisingly, although there was no difference in extent of resection between the groups (gross total resection (GTR), 96.26% vs. 96.15%, p= 0.45), patients with sNF2 tumors had more associated deaths (14.6% vs. 0%, p= 0.03) and a marginally shorter overall survival (p= 0.061). GTR was associated with longer progression-free survival (p= 0.037). CONCLUSION Within the homogeneous group of somatic NF2 mutated meningiomas, infratentorial tumors are seemingly more benign in their genomic make-up and clinical manifestation as compared to ones located in the supratentorial location. While GTR is useful to both groups in preventing recurrence, this benefit may be especially important in the clinically and genomically higher risk sNF2 tumors.
ANGI-02. EPIGENETIC REGULATION OF GLIOMA INVASION BY CHITINASE-3-LIKE PROTEIN 1 (CHI3L1) CPG PROMOTER METHYLATION
Authors: Sophie Schreiner, Camille Cialini, Uxue Salcedo, Michel Mittelbronn, Ann-Christin Hau, Tanja Müller
Journal: Neuro-Oncology (2022)

Abstract Epigenetically controlled processes play an important role in development but also in the formation and progression of many common diseases. Molecular signatures are increasingly incorporated into cancer classifications and DNA methylation-based analyses of brain tumors including glioma is currently the gold standard. Glioblastoma (GBM), CNS WHO grade 4, is characterized by a very diffuse infiltrative growth into the adjacent brain parenchyma. Due to these highly invasive but also genetically heterogeneous and plastic cellular phenotypes, standard treatment, including maximum resection, radio- and chemotherapy, has limited efficacy. It can be assumed that intertumoral or molecular heterogeneity of gliomas at the transcriptome level is caused by altered epigenetic changes within the individual tumor cells. Considering this, we hypothesize that tumor cell invasion being one of the major hallmarks of highly malignant gliomas can be associated with altered DNA methylation and therefore transcript expression. To analyze this, we isolated fractions of glioma cells with increased invasive properties and performed Illumina® array-based methylation profiling as well as RNA sequencing analysis to identify methylation-driven, invasion-promoting genes. Among other, we focused on Chitinase-3-like protein 1 (CHI3L1) as a candidate gene with significantly decreased promoter methylation in invasive cell fractions and overall strong transcript expression in high-grade gliomas. Differential expression and methylation correlation of TCGA data combined with our own dataset revealed that CHI3L1 expression is dependent on the methylation status of at least three CpG sites within the gene promoter region. We validated these findings using several in vitro experimental settings and propose an upstream regulatory mechanism in which single CpG DNA demethylation within the CHI3L1 promoter facilitates transcription factor binding resulting in gene expression.
EPID-13. CHARACTERIZATION OF PEDIATRIC RADIATION-INDUCED MENINGIOMA: A SEER ANALYSIS
Authors: Jashanjeet Matharoo, Jefferson Abaricia, Charles Opalak, William Broaddus
Journal: Neuro-Oncology (2022)

Abstract OBJECTIVE Radiation-induced meningiomas (RIM) are the most common secondary neoplasm arising from radiation therapy. RIM have not been characterized in pediatric populations on a national scale despite displaying shorter latency and higher malignancy rates in institutional studies. The objective of this study was to characterize pediatric RIM and compare latency and malignancy rates to those of adult RIM using the National Cancer Institute’s Surveillance, Epidemiology and End Results Program (SEER) database. METHODS From the SEER Research Plus Nov 2020 (1975-2018) dataset, 56161 patients treated with EBRT for ocular/orbital tumors, brain/nervous system tumors, and leukemia were identified. 185 patients meeting criteria for RIM were selected: cranial/spinal EBRT (presumed from diagnostic indication), histologically distinct precedent tumor treated with EBRT, and a minimum 5-year latency from EBRT to meningioma diagnosis. This sub-population was divided into 2 groups – pediatric (ages 0-19, n = 10) and adult (ages &amp;gt; 20, n = 175) RIM – and latency, recurrence rate and multiplicity were compared for each group. The number of tumors classified as malignant (as opposed to benign or borderline malignant) was also compared between groups. Additionally, demographic data were compared for each group. RESULTS Of the pediatric RIM patients, 70% were male, 70% were Caucasian, and 10% were African American. No pediatric RIM patients experienced a recurrence or presented with multiple RIMs. The pediatric group showed lower latency (11.00 ± 1.94 years, p &amp;lt; 0.001) and a higher malignancy rate (30%, p = 0.002) than the adult group (latency of 23.38 ± 8.69 years; malignancy rate 5.1%). CONCLUSION These data represent the first characterization of pediatric RIM from a national database and support prior findings of shorter latency and higher malignancy rates in pediatric vs adult RIM, as well as lay the groundwork for future nationwide monitoring of this rare yet highly significant complication.
BIOM-28. AN EXOSOME BASED LIQUID BIOPSY DIAGNOSTIC FOR GLIOMA
Authors: Amit Ray, Rahul Lath, Madhan Reddy, Kaushal Ippili, Boola Ratnam, Tarang Vohra, Arjun Reddy, Brahma Prasad, Alok Ranjan, Rajesh Reddy, Manas Panigrahi, Venkateshwara Rao, Anandh Balasubramanium, Inderjeet Kaur
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Liquid biopsy has gained popularity of late in the diagnosis and management of several cancers. This study aims to diagnose suspected lesions suspected of being gliomas on neuro-imaging by obtaining a peripheral venous blood sample- with a specificity and sensitivity that approaches a tissue biopsy. MATERIALS AND METHODS After clearance from Ethics Committees, specimens of the tumour tissue along with blood from a peripheral or vein was collected from all 80 adult patients with a suspected diagnosis of glioma. Clinical details along with the neurological status, the functional score, the extent of resection, pathological diagnosis and survival data were also collected. The tumour tissue transported in RNA-later and stored at -80C. Following exosome isolation, RNA-seq was performed on the exosomal sample obtained from the serum and the tumour sample. Exome analysis was performed on the tumour tissue (somatic mutations) and the WBC (for germline mutations) to a depth of 100. RESULTS The analysed data was quality checked for all glioma associated genes including but not limited to ATRX, H3F3A, IDH1, MGTM and TERT driver genes related to DNA repair, cytoskeleton and cellular proliferation-related genes EGFR, FLT1/(VEGFR), BRAF, GFAP, MKi67, NES, OLIG2, PIK3CA, SMAD3, S1001A and VIM and tumour suppressor genes SMARCB1/INI1 and TP53. Open-source cloud based genomic analysis platforms were used for analysis. Machine learning clustering algorithms identified serum exosome based clusters that corresponded to already identified glioma tissue based genomic subgroups, with specificity and sensitivity approaching 95%. CONCLUSION Liquid biopsies provide a reliable and effective way of diagnosing gliomas in patients who present with an intracranial lesion on radiology.
DDDR-13. MGMT FUNCTION DETERMINES THE DIFFERENTIAL RESPONSE OF ATR AND PARP INHIBITORS WITH DNA DAMAGING AGENTS FOR GBM THERAPY
Authors: Dimpy Koul, Shaofang Wu, Xaolong Li, Sabbir Khan, Veerakumar Balasubramaniyan, W K Alfred Yung
Journal: Neuro-Oncology (2022)

Abstract The most common cancer therapies including chemo- and radiation therapy are designed to induce cell death by DNA damage. However, DNA damage response (DDR) repair pathways initiated by tumor cells can resist the effect of anticancer drugs thus providing the rationale for combining DNA repair pathway inhibitors with radiation and DNA damaging anticancer drugs. The reliance of different cancer to different DDR mechanism can guide for targeted use of specific DDR inhibitor to maximize tumor cell killing. Here, we show the differential activities of two classes of DDR pathway inhibitors, Ataxia Telangiectasia- and Rad3-related kinase (ATRi) and poly(ADP-ribose) polymerases inhibitors (PARPi) across 20 glioma stem cell (GSC) lines. Using a panel of 3 ATRi, we identified a subgroup of GSCs, showing significant synergism with TMZ combination but resistant to ATRi single agent monotherapy. Interestingly, majority of the synergistic cell lines are associated with MGMT promoter methylation, suggesting that only tumor cells with no MGMT repair will benefit from ATR inhibition. Moreover, we also observe that PARPi + TMZ showed synergism only in MGMT unmethylated GSC cells suggesting that this synergism is a result of the dual function of PARPi in blocking BER repair and blocking MGMT PARylation thus abolishing MGMT mediated repair. Altogether, we believe MGMT methylation status in primary GBM could function as a strong biomarker for patient selection for ATRi or PARPi combination with TMZ in the clinic. We are currently exploring the activity of the triple combination of TMZ + PARPi + ATRi for the small subgroup of GSCs that do not show response to either TMZ + ATRi or PARPi + TMZ combinations.
IMMU-21. GLIOMA-DERIVED FACTORS RECRUIT AND INDUCE AN IMMUNE SUPPRESSIVE PHENOTYPE IN BONE MARROW-DERIVED CCR2+ MYELOID CELLS
Authors: Gregory Takacs, Christian Kreiger, Defang Luo, Guimei Tian, Loic Deleyrolle, Jeffrey Harrison
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION Infiltrating immune-suppressive myeloid cells represent a tumor supportive population that contributes to immune checkpoint inhibitor resistance and poor survival in Glioblastoma (GBM) patients. We have previously characterized monocytic-myeloid derived suppressor cells (M-MDSCs) based on their dual expression of chemokine receptors CCR2 and CX3CR1(CCR2+/CX3CR1+). Genetic and pharmacologic targeting of CCR2, in combination with PD-1 blockade, reduced the percentage of M-MDSCs in the glioma-microenvironment and slowed the progression of KR158 and 005GSC murine gliomas. Additional studies are needed to investigate the chemokines responsible for the tumor recruitment of CCR2+/CX3CR1+ cells and the impact of glioma derived factors on their immune suppressive phenotype. OBJECTIVE Evaluate the effect of glioma derived factors on the migration and suppression of bone marrow CCR2+/CX3CR1+ myeloid cells. METHODS A transwell migration assay was utilized to determine the migratory ability of CCR2+/CX3CR1+ cells to KR158B conditioned in the presence of CCL2 and CCL7 neutralizing antibodies. Ly6G-/GR1+ cells were isolated from bone marrow cultured with KR158B conditioned media and co-cultured with freshly isolated T-cells to examine their immune-suppressive phenotype. RESULTS KR158B gliomas differentially upregulate cytokines including CCL2, IL6, G-CSF, GM-CSF as compared to healthy naive brains. KR158B conditioned media increased the percentage of bone marrow-derived CCR2+/CX3CR1+ cells that are CD11b+, Ly6Chi, and Ly6G-. Bone marrow-derived CCR2+/CX3CR1+ cells expanded in KR158B condition media suppress both CD4+ and CD8+ T cell proliferation. Bone marrow-derived CCR2+/CX3CR1+ cells migrate to recombinant CCL2 and CCL7 as well as KR158B glioma conditioned media. Migration to conditioned media is completely inhibited by the combination of CCL2 and CCL7 neutralizing antibodies. High CCL2 and CCL7 are associated with poor prognosis in human GBM. CONCLUSION Glioma-derived CCL2 and CCL7 mediate migration of CCR2+ myeloid cells into the tumor microenvironment in a redundant manner. Additional glioma-derived factors induce CCR2+/CX3CR1+ myeloid cells to a CD4/8+ T cell suppressive state.
IMMU-13. PROMOTER DEMETHYLATION OF NY-ESO-1 PRIMES GLIOBLASTOMA FOR IMMUNOTHERAPEUTIC TARGETING
Authors: Thomas Lai, Janet Treger, Jingyou Rao, Lu Sun, Tie Li, Albert Lai, Robert Prins, Richard G Everson
Journal: Neuro-Oncology (2022)

Abstract INTRODUCTION New York-esophageal squamous cell carcinoma (NY-ESO-1) specific adoptive T-cell immunotherapy is an appealing strategy for the treatment of gliomas because it elicits a strong antibody and T-cell response and is downregulated in most normal adult tissues which produces an effective and specific antitumor response. However, NY-ESO-1 is often poorly expressed in GBM, presumably through promoter methylation. Neither the prevalence of NY-ESO-1 downregulation in glioblastoma (GBM) patient tumors nor the presumed mechanism of downregulation by promoter methylation have been formally established. METHODS We characterized baseline CpG methylation of NY-ESO-1 in patient GBM samples using bisulfite sequencing. We induced NY-ESO-1 expression in vitro in human GBM cell lines (U251) and patient-derived gliomaspheres using the demethylating agent decitabine (DAC). We investigated the epigenetic response of DAC treated GBM cell lines with bisulfite sequencing and NY-ESO-1 expression with quantitative real time PCR. Lastly, we performed single cell RNA sequencing on DAC treated and untreated U251 and PGDSC to evaluate tumor subpopulations that upregulate NY-ESO-1 and co-expressed cancer testis antigens after DAC treatment. RESULTS NY-ESO-1 expression is associated with promoter methylation in the majority of GBM. Prolonged low dose of DAC explicitly demethylated the promoter region of NY-ESO-1 and resulted in robust mRNA expression. DAC treatment co-expresses NY-ESO-1 with other cancer testis antigens CTAG2 and MAGEA4 as demonstrated by single cell RNA sequencing. CONCLUSION These results reveal a feasible strategy of cancer testis antigen promoter demethylation which creates an inducible tumor antigen for immunotherapeutic targeting. We speculate that DAC induced upregulation of NY-ESO-1 and co-expressed cancer testis antigens renders tumor recognition by NY-ESO-1 specific T cells.
IMMU-22. REPROGRAMMING OF MICROGLIA/MACROPHAGES IN GLIOBLASTOMA IMPROVES ANTI-TUMOR T CELL RESPONSES
Authors: Valentina Fermi, Rolf Warta, Carmen Rapp, Philip Dao Trong, Gerhard Jungwirth, Unterberg Andreas, Christel Herold-Mende
Journal: Neuro-Oncology (2022)

Abstract Glioma-infiltrating myeloid cells such microglia and macrophages (GAM) are a major component of the immunosuppressive tumor microenvironment in glioblastoma (GBM). Especially their anti-inflammatory M2-like activation state might counteract efficacy of immunotherapeutic interventions by impairing effector T cell infiltration and function. Therefore, we studied the ability of the small molecule inhibitors (SMI) PLX3397, BLZ945, and GW2580 that target the M2-associated colony stimulating factor-1 receptor (CSF1R) to shape GAM phenotype towards a pro-inflammatory M1-like phenotype and how this affects the T cell compartment.Upon treatment of freshly isolated CD11b-sorted GBM patient-derived GAMs (n = 15) a decreased expression of CD163 (M2-like) and an increased expression of HLA-DR (M1-like) as well as an increased nitrite production as an indirect measure for iNOS activation (M1-like) was observed which was most pronounced for BLZ945, and GW2580. Transcriptome analysis of treated vs. untreated GAMs supported a reprogramming towards a pro-inflammatory phenotype. In addition, treatment of GAMs in a GBM patient-derived tumor organoid model confirmed a substantial decrease of CD163+ M2-polarized GAM together with a reduced number of proliferating tumor cells. Finally, treatment of patient-derived GAMs led to an increased T cell transmigration through a dense barrier of autologous tumor-derived endothelial cells and increased the ability of T cells to kill autologous tumor cells. Our results support CSF1R blockade is able to reduce the immunosuppressive and pro-tumorigenic functions of GAM substantially and thereby could enhance the effectiveness of T cell-based immunotherapy.
EPID-15. SURGICAL RESECTION OF BENIGN MENINGIOMAS IN THE ELDERLY POPULATION: IMPLICATIONS FROM A PROPENSITY-SCORE MATCHED ANALYSIS
Authors: Jun Ma, Ping Zhu, Clark Chen
Journal: Neuro-Oncology (2022)

Abstract Object We characterized the patterns of clinical practice in benign meningioma resection and survival outcome as a function of patient age using the Surveillance, Epidemiology and End Results (SEER) and the SEER-Medicare database. METHODS The likelihood for recommendation to proceed with resection and survival in adult, benign meningioma patients were characterized using logistic regression. Survival analysis was performed using a propensity-score matching (PSM)-method (covariates balanced in PSM: socio-demographics, facility features, and comorbidities) through a multivariable logistic regression and accelerated failure time (AFT) models. RESULTS The likelihoods of recommendation for surgery were 0.59 (95%CI = 0.53-0.66, P &amp;lt; 0.001) and 0.17 (95%CI = 0.15-0.21, P &amp;lt; 0.001) for meningioma patients age 60-79 and ≥ 80, relative to patients age 40-59. Expectedly, the hazard of death increased with advancing aging strata in patients who underwent meningioma resection. To account for mortality risk associated with normal aging, a PSM analysis was performed to calculate the hazard of death for surgically resected meningioma patients relative to an age- and PSM-matched cancer-free patient cohort. This odds ratio (OR) was 3.84 (95%CI: 3.15-4.67, P &amp;lt; 0.001) for patients age 60-79 and 3.41 (95%CI: 2.56-4.56, P &amp;lt; 0.001) for patients age ≥ 80. These two ORs were not statistically different (ROR: 0.89, 95%CI: 0.63-1.62, P = 0.512), suggesting that the likelihood of death after benign meningioma resection was not significantly elevated in patients age ≥ 80 after accounting for expected age-related mortality. CONCLUSION Our study suggests that surgeons exert caution in selecting elderly with meningioma for resection. After accounting for mortality risk associated with normal aging and patient selection by the surgeon, the likelihood of death for patients age ≥ 80 who underwent meningioma resection was comparable to that observed for patients age 60-79.